| fastq10x_qc_analysis |
1 |
- results/fastq10x/fastq10x_qc_analysis.ipynb
- results/fastq10x/fastq10x_qc_analysis.html
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| align_fastq10x_summary |
1 |
- results/aligned_fastq10x/align_fastq10x_summary.ipynb
- results/aligned_fastq10x/align_fastq10x_summary.html
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| fastq10x_transcript_coverage |
1 |
- results/aligned_fastq10x/fastq10x_transcript_coverage.ipynb
- results/aligned_fastq10x/fastq10x_transcript_coverage.html
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| viral_fastq10x_coverage |
1 |
- results/viral_fastq10x/viraltag_locs.csv
- results/viral_fastq10x/viralbc_locs.csv
- results/viral_fastq10x/viral_fastq10x_coverage.ipynb
- results/viral_fastq10x/viral_fastq10x_coverage.html
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| analyze_gaps |
1 |
- results/viral_fastq10x/gap_analysis.ipynb
- results/viral_fastq10x/gap_analysis.html
- results/viral_fastq10x/gapped_reads.csv
- results/viral_fastq10x/gapped_reads_summary.csv
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| count_viraltags_fastq10x |
5 |
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_wt_rapidpilot.ipynb
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_wt_rapidpilot.html
- results/viral_fastq10x/viraltag_counts_hashing_wt_rapidpilot.csv
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial1.ipynb
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial1.html
- results/viral_fastq10x/viraltag_counts_hashing_trial1.csv
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial2.ipynb
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial2.html
- results/viral_fastq10x/viraltag_counts_hashing_trial2.csv
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial3_withNH4Cl.ipynb
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial3_withNH4Cl.html
- results/viral_fastq10x/viraltag_counts_hashing_trial3_withNH4Cl.csv
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial3_noNH4Cl.ipynb
- results/viral_fastq10x/count_viraltags_fastq10x-hashing_trial3_noNH4Cl.html
- results/viral_fastq10x/viraltag_counts_hashing_trial3_noNH4Cl.csv
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| count_viralbc_fastq10x |
5 |
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_wt_rapidpilot.ipynb
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_wt_rapidpilot.html
- results/viral_fastq10x/viralbc_counts_hashing_wt_rapidpilot.csv
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial1.ipynb
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial1.html
- results/viral_fastq10x/viralbc_counts_hashing_trial1.csv
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial2.ipynb
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial2.html
- results/viral_fastq10x/viralbc_counts_hashing_trial2.csv
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial3_withNH4Cl.ipynb
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial3_withNH4Cl.html
- results/viral_fastq10x/viralbc_counts_hashing_trial3_withNH4Cl.csv
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial3_noNH4Cl.ipynb
- results/viral_fastq10x/count_viralbc_fastq10x-hashing_trial3_noNH4Cl.html
- results/viral_fastq10x/viralbc_counts_hashing_trial3_noNH4Cl.csv
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| analyze_cell_gene_matrix |
5 |
- results/analysis/hashing_wt_rapidpilot_analyze_cell_gene_matrix.ipynb
- results/analysis/hashing_wt_rapidpilot_analyze_cell_gene_matrix.html
- results/analysis/hashing_trial1_analyze_cell_gene_matrix.ipynb
- results/analysis/hashing_trial1_analyze_cell_gene_matrix.html
- results/analysis/hashing_trial2_analyze_cell_gene_matrix.ipynb
- results/analysis/hashing_trial2_analyze_cell_gene_matrix.html
- results/analysis/hashing_trial3_withNH4Cl_analyze_cell_gene_matrix.ipynb
- results/analysis/hashing_trial3_withNH4Cl_analyze_cell_gene_matrix.html
- results/analysis/hashing_trial3_noNH4Cl_analyze_cell_gene_matrix.ipynb
- results/analysis/hashing_trial3_noNH4Cl_analyze_cell_gene_matrix.html
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| make_fastq10x |
7 |
- results/fastq10x/hashing_wt_rapidpilot-2019-12-03_all_R1.fastq.gz
- results/fastq10x/hashing_wt_rapidpilot-2019-12-03_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_wt_rapidpilot-2019-12-03
- results/fastq10x/hashing_wt_rapidpilot-2019-12-03_qc_stats.csv
- _mkfastq_hashing_wt_rapidpilot-2019-12-03.csv
- __hashing_wt_rapidpilot-2019-12-03.mro
- results/fastq10x/hashing_trial1-2020-01-16_all_R1.fastq.gz
- results/fastq10x/hashing_trial1-2020-01-16_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_trial1-2020-01-16
- results/fastq10x/hashing_trial1-2020-01-16_qc_stats.csv
- _mkfastq_hashing_trial1-2020-01-16.csv
- __hashing_trial1-2020-01-16.mro
- results/fastq10x/hashing_trial1-2020-02-18_all_R1.fastq.gz
- results/fastq10x/hashing_trial1-2020-02-18_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_trial1-2020-02-18
- results/fastq10x/hashing_trial1-2020-02-18_qc_stats.csv
- _mkfastq_hashing_trial1-2020-02-18.csv
- __hashing_trial1-2020-02-18.mro
- results/fastq10x/hashing_trial2-2020-06-02_all_R1.fastq.gz
- results/fastq10x/hashing_trial2-2020-06-02_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_trial2-2020-06-02
- results/fastq10x/hashing_trial2-2020-06-02_qc_stats.csv
- _mkfastq_hashing_trial2-2020-06-02.csv
- __hashing_trial2-2020-06-02.mro
- results/fastq10x/hashing_trial2-2020-07-01_all_R1.fastq.gz
- results/fastq10x/hashing_trial2-2020-07-01_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_trial2-2020-07-01
- results/fastq10x/hashing_trial2-2020-07-01_qc_stats.csv
- _mkfastq_hashing_trial2-2020-07-01.csv
- __hashing_trial2-2020-07-01.mro
- results/fastq10x/hashing_trial3_withNH4Cl-2020-07-24_all_R1.fastq.gz
- results/fastq10x/hashing_trial3_withNH4Cl-2020-07-24_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_trial3_withNH4Cl-2020-07-24
- results/fastq10x/hashing_trial3_withNH4Cl-2020-07-24_qc_stats.csv
- _mkfastq_hashing_trial3_withNH4Cl-2020-07-24.csv
- __hashing_trial3_withNH4Cl-2020-07-24.mro
- results/fastq10x/hashing_trial3_noNH4Cl-2020-07-24_all_R1.fastq.gz
- results/fastq10x/hashing_trial3_noNH4Cl-2020-07-24_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/hashing_trial3_noNH4Cl-2020-07-24
- results/fastq10x/hashing_trial3_noNH4Cl-2020-07-24_qc_stats.csv
- _mkfastq_hashing_trial3_noNH4Cl-2020-07-24.csv
- __hashing_trial3_noNH4Cl-2020-07-24.mro
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| align_fastq10x |
5 |
- results/aligned_fastq10x/hashing_wt_rapidpilot/Solo.out/Gene/Summary.csv
- results/aligned_fastq10x/hashing_wt_rapidpilot/Solo.out/Gene/UMIperCellSorted.txt
- results/aligned_fastq10x/hashing_wt_rapidpilot/Solo.out/Gene/filtered/matrix.mtx
- results/aligned_fastq10x/hashing_wt_rapidpilot/Solo.out/Gene/filtered/features.tsv
- results/aligned_fastq10x/hashing_wt_rapidpilot/Solo.out/Gene/filtered/barcodes.tsv
- results/aligned_fastq10x/hashing_wt_rapidpilot/Aligned.sortedByCoord.out.bam
- results/aligned_fastq10x/hashing_trial1/Solo.out/Gene/Summary.csv
- results/aligned_fastq10x/hashing_trial1/Solo.out/Gene/UMIperCellSorted.txt
- results/aligned_fastq10x/hashing_trial1/Solo.out/Gene/filtered/matrix.mtx
- results/aligned_fastq10x/hashing_trial1/Solo.out/Gene/filtered/features.tsv
- results/aligned_fastq10x/hashing_trial1/Solo.out/Gene/filtered/barcodes.tsv
- results/aligned_fastq10x/hashing_trial1/Aligned.sortedByCoord.out.bam
- results/aligned_fastq10x/hashing_trial2/Solo.out/Gene/Summary.csv
- results/aligned_fastq10x/hashing_trial2/Solo.out/Gene/UMIperCellSorted.txt
- results/aligned_fastq10x/hashing_trial2/Solo.out/Gene/filtered/matrix.mtx
- results/aligned_fastq10x/hashing_trial2/Solo.out/Gene/filtered/features.tsv
- results/aligned_fastq10x/hashing_trial2/Solo.out/Gene/filtered/barcodes.tsv
- results/aligned_fastq10x/hashing_trial2/Aligned.sortedByCoord.out.bam
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Solo.out/Gene/Summary.csv
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Solo.out/Gene/UMIperCellSorted.txt
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Solo.out/Gene/filtered/matrix.mtx
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Solo.out/Gene/filtered/features.tsv
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Solo.out/Gene/filtered/barcodes.tsv
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Aligned.sortedByCoord.out.bam
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Solo.out/Gene/Summary.csv
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Solo.out/Gene/UMIperCellSorted.txt
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Solo.out/Gene/filtered/matrix.mtx
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Solo.out/Gene/filtered/features.tsv
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Solo.out/Gene/filtered/barcodes.tsv
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Aligned.sortedByCoord.out.bam
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| index_bam |
5 |
- results/aligned_fastq10x/hashing_wt_rapidpilot/Aligned.sortedByCoord.out.bam.bai
- results/aligned_fastq10x/hashing_trial1/Aligned.sortedByCoord.out.bam.bai
- results/aligned_fastq10x/hashing_trial2/Aligned.sortedByCoord.out.bam.bai
- results/aligned_fastq10x/hashing_trial3_withNH4Cl/Aligned.sortedByCoord.out.bam.bai
- results/aligned_fastq10x/hashing_trial3_noNH4Cl/Aligned.sortedByCoord.out.bam.bai
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| samtools index {input} {output}
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| make_refgenome |
1 |
- results/genomes/cell_and_virus_gtf.gtf
- results/genomes/refgenome
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|
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| cat {input.cell_gtf} {input.viral_gtf} > {output.concat_gtf}
mkdir -p {output.genomeDir}
STAR --runThreadN {threads} --runMode genomeGenerate --genomeDir {output.genomeDir} --genomeFastaFiles {input.cell_genome} {input.viral_genome} --sjdbGTFfile {output.concat_gtf}
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| get_cb_whitelist_10x |
1 |
- results/aligned_fastq10x/cb_whitelist_10x.txt
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|
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| if [[ {params.url} == *.gz ]]
then
wget -O - {params.url} | gunzip -c > {output}
else
wget -O - {params.url} > {output}
fi
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| get_cell_genome |
1 |
- results/genomes/cell_genome.fasta
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| wget -O - {params.ftp} | gunzip -c > {output}
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| get_cell_gtf |
1 |
- results/genomes/cell_gtf.gtf
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|
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| wget -O - {params.ftp} | gunzip -c > {output}
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